Research Publications

2006 Publication list




Adams, B.J., Bardgett, R.D., Ayres, E., Wall, D.H., Aislabie, J., Bamforth, S., Bargagli, R., Cary, C., Cavacini, P., Connell, L., Convey, P., Fell, J.W., Frati, F., Hogg, I.D., Newsham, K.K., O'Donnell, A., Russell, N., Seppelt, R.D., and Stevens, M.I. Diversity and Distribution of Victoria Land Biota.  Soil Biology and Biochemistry, 38: 3003-3018.
Auch, A.F., Henz, S.R., Holland, B.R., and Göker, M. Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences.  BMC Bioinformatics 7:350.
Barnes, S.S., Matisoo-Smith, E., and Hunt, T. Ancient DNA of the Pacific Rat (Rattus exulans) from Rapa Nui (Easter Island).  Journal of Archaeological Science 33:1536-1540.
Baroni, M., Semple, C., and Steel, M. Hybrids in real time.  Systematic Biology 44(1): 46-56: 2006.
Baroni, M. and Steel, M. Accumulation phylogenies.  Annals of Combinatorics 10: 19-30.
Birchard, G.F., Nelson, N.J., and Daugherty, C.H.  A circadian rhythm in oxygen consumption rate in juvenile tuatara (Sphenodon punctatus). New Zealand Journal of Zoology 33: 185-188.
Burnham, D.K., Keall, S.N., Nelson, N.J., and Daugherty, C.H. Effects of sampling date, gender, and tick burden on peripheral blood cells of captive and wild tuatara (Spendodon punctatus).  New Zealand Journal of Zoology 33: 241-248.
Chan, C., Ballantyne, K.N., Aikman, H., Chambers, G.K., and Daugherty, C.H Conservation genetics of the Forbes parakeet (Cyanoramphus forbesi) on Mangere Island, Chatham Islands.  DOC Research & Development Series 254. 
Chan, C., Ballantyne, K.N., Aikman, H., Fastier, D., Chambers, G.K., and Daugherty, C.H. Genetic analysis of interspecific hybridisation in the world’s only Forbes’ parakeet (Cyanoramphus forbesi) natural population.  Conservation Genetics (7): 493-506.
Chan, Z., Collins, L. and Kasabov, N. An efficient greedy K-means algorithm for global gene trajectory clusterin.  Expert Systems with Applications. 30 (1) 137-141.
Chan, Z.S.H., Kasabov, N. and Collins, L. A two-stage methodology for gene regulatory network extraction from time-course gene expression data.  Expert Systems with Applications30:59-63.
Chor, B., Hendy, M.D. and Snir, S. Maximum Likelihood Jukes-Cantor Triplets: Analytic Solutions. Molecular Biology and Evolution, 23: 626-632.
Clarke, A.C., Burkenshaw, M., McLenachan, P.A., Erickson, D. and Penny, D. Reconstructing the origins and dispersal of the Polynesian bottle gourd (Lagenaria siceraria).  Molecular Biology and Evolution 23: 893-900.
Collins, L.J. and Penny, D. Investigating the intron recognition mechanism in eukaryotes.  Molecular Biology and Evolution. 23: 901-910.
Dress, A. and Steel, M. Mapping edge sets to splits in trees: the path index and parsimony.  Annals of Combinatorics 10: 77-96.
Donald, K.M. and Spencer, H.G. Polymorphic microsatellite DNA markers in the mudflat topshell Diloma subrostrata (Gastropoda, Trochidae).  Molecular Ecology Notes (6): 762-764.
Ewing, G. and Rodrigo, A.G. Estimating Population Parameters using the Structured Serial Coalescent with Bayesian MCMC Inference when some Demes are Hidden.  Evolutionary Bioinformatics Online 2:239-247.
Gartrell, B.D., Jillings, E., Adlington, B., Mack, H. and Nelson, N.J.   Health screening for a translocation of captive-reared tuatara (Sphenodon punctatus) to an island refuge.   New Zealand Veterinary Journal 54(6): 344-349.
Gartrell, B., Morgan, K., Owen, M., Hartman, A., Keall, S.N., and Khull, M. Computed tomographic evaluation of the skulls of three captive tuatara. Conference Proceedings of the Annual Meeting of the Unusual and Exotic Pets group of the Australian Veterinary Association, pp 41-46.
Gascuel, O. and Steel, M. Neighbor-Joining revealed.  Molecular Biology and Evolution23(11): 1997-2000.
Gernhard, T., Ford, D., Vos, R., and Steel, M. Estimating the relative order of speciation or coalescence events on a given phylogeny.  Evolutionary Bioinformatics Online 2: 309-317.
Guindon, S., Black, M., and Rodrigo, A.  Control of the false discovery rate applied to the detection of positively selected amino acid sites.  Mol. Biol. Evol. 23(5):919-926.
Hare, K.M., Pledger, S., Thompson, M.B., Miller, J.H., and Daugherty, C.H. Daily patterns of metabolic rate among New Zealand lizards (Reptilia: Lacertilia: Diplodactylidae & Scincidae).  Physiological and Biochemical Zoology 79: 745-753.
Hartmann, K. and Steel, M. Maximimizing phylogenetic diversity in biodiverstity conservation: greedy solutions to the Noah's Ark problem.  Systematic Biology 55(4), 644-651.
Hoare, J.M. and Hare, K.M. Hoplodactylus maculatus (Common Gecko) toxin consumption.  Herpetological Review 37(1): 86-87.
Hoare, J.M. and Hare, K.M. The impact of brodifacoum on non-target wildlife: gaps in knowledge.  New Zealand Journal of Ecology 30(2): 157-167
Hoare, J.M. and Nelson, N.J. Hoplodactylus maculatus (Common Gecko) social assistance. Herpetological Review 37(2): 222-223.
Hoare, J.M., Pledger, S., Keall, S.N., Nelson, N.J., Mitchell, N.J. and Daugherty, C.H. Conservation implications of a long-term decline in body condition in the Brothers Island tuatara, Sphenodon guntheri.  Animal Conservation 9: 456-462.
Hogg, I.D., Cary, S.C., Convey, P., Newsham, K.K., O'Donnell, A.G., Adams, B.J., Aislabie, J., Frati, F., Stevens, M.I.,Wall, D.H. Biotic interactions in Antarctic terrestrial ecosystems: are they a factor?  Soil Biology & Biochemistry, 38: 3035-3040.
Holland, B.R., Jermiin, L.S., and Moulton, V. Improved consensus network techniques for genome-scale phylogeny.  Molecular Biology and Evolution 23: 848-855.
Jeffares, D.C., Mourier, T and Penny, D. The biology of intron gain and loss.  TRENDS in Genetics 22 (1): 16-22.
Johnson, K.P., Kennedy, M. and McCracken, K.G. Reinterpreting the Origins of Flamingo Lice: Cospeciation or Host-Switching?  Biology Letters 2: 275-278.
Kurland, C.G., Collins, L.J., and Penny, D. Genomics and the Irreducible Nature of Eukaryote Cells.  Science 312: 1011-1014.
Lambert, D.M. and Millar, C.D. Large-scale ancient genomics is born!  Nature 444:275-276.
Lysak, M.A., Berr, A., Pecinka, A., Schmidt, R., McBreen, K. and Schubert, I. Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species.  PNAS 103:5224-5229.
McCallum, J., Clarke, A., Pither-Joyce, M., Shaw, M., Butler, R., Brash, D., Scheffer, J., Sims, I., van Heusden, S., Shigyo, M. and Havey, M. J. Genetic mapping of a major gene affecting onion bulb fructan content.  Theoretical and Applied Genetics 112(5): 958-967.
McGaughran, A., Hogg, I.D., Stevens, M.I., Chadderton, W.L.and Winterbourn, M.J. Genetic divergence of three freshwater isopod species from southern New Zealand.  Journal of Biogeography 33: 23-30.
MacAvoy, E.S., McGibbon, L.M., Sainsbury, J.P., Lawrence, H., Wilson, C.A., Daugherty, C.H. and Chambers, G.K. Genetic variation in island populations of tuatara (Sphenodon spp.) inferred from microsatellite markers.  Conservation Genetics 8(2): 305-318.
Matheson, J.W., Rich, F.J., Corbett, C., Greenwood, K., Huang, Q.S., Penny, D., and Hendy, M.D. Distinct patterns of evolution between respiratory syncytial virus subgroups A and B from New Zealand isolates collected over thirty-seven years.  J Medical Virology 78:1354-1364.
Meudt, H.M. A revision of the genus Ourisia (Plantaginaceae).  Systematic Botany Monographs 77: 1-188.
Meudt, H.M. and Simpson, B.B. The biogeography of subalpine, austral Ourisia (Plantaginaceae) based on molecular phylogenetic evidence: South American origin and dispersal to New Zealand and Tasmania.  Biological Journal of the Linnean Society 87: 479-513.
Miller, H.C. Cloacal and buccal swabs are a reliable source of DNA for microsatellite genotyping of reptiles.   Conservation Genetics 7: 1001-1003. 
Miller, H.C., Belov, K., and Daugherty, C.H. MHC class I genes in the tuatara (Sphenodon spp.): Evolution of the MHC in an ancient reptilian order.  Molecular Biology and Evolution 23: 949-956.
Miller, H.C., and Lambert, D.M. A molecular phylogeny of New Zealand’s Petroica (Aves: Petroicidae) species based on mitochondrial DNA sequences.  Molecular Phylogenetics and Evolution 40: 844-855.
Mitchell, N.J., Nelson, N.J., Cree, A., Pledger, S., Keall, S.N., and Daugherty, C.H. Support for a rare pattern of temperature-dependent sex determination in archaic reptiles: evidence from two species of tuatara (Sphenodon).  Frontiers in Zoology 3:9.
Moore, J.A. and Godfrey, S.S. Sphenodon punctatus (common tuatara). Opportunistic predation.  Herpetological Review 37(1): 81-82.
Nelson, N.J., Thompson, M.B., Pledger, S., Keall, S.N., and Daugherty, C.H.   Performance of juvenile tuatara depends on age, clutch and incubation regime.   Journal of Herpetology 40(3): 399-403.
Nielson, M., Lohman, K., Daugherty, C.H., Allendorf, F.W., Knudsen, K.L., and Sullivan, J. Allozyme and mitochondrial DNA variation in the tailed frog (Anura: Ascaphus): The influence of geography and gene flow.  Herpetologica 62 (3), 235-258.
Nolan L., Hogg, I.D., Stevens, M.I., and Haase, M. Fine scale distribution of mtDNA haplotypes for the springtail Gomphiocephalus hodgsoni (Collembola) corresponds to an ancient shoreline in Taylor Valley, continental Antarctica Polar Biology 29: 813-819.
Penny, D. Why the resistance?  EMBO report. Vol 7,no 10: 975.
Phillips, M.J. Sympathy for the Devil.  Nature 440.
Phillips, M.J., McLenachan, P.A., Down, C., Gibb, G.C. and Penny, D. Combined nuclear and mitochondrial protein -coding DNA sequences resolve the interrelations of the major Australasian marsupial radiations.  Systematic Biology 55: 122-137.
Poss, M., Ross, H.A., Painter, S.L., Holley, D.C., Terwee, J.A., Vandewoude, S., and Rodrigo, A.G. Feline lentivirus evolution in cross-species infection reveals high error burdens and selection on key residues in the viral polymerase.  Journal of Virology 80:2728-2737.
Robins, J.H., Ross, H.A., Allen, M.S., Matisoo-Smith, E.M. Sus bucculentus revisited. Nature 440.
Ross, H.A., Nickle, D.C., Liu. Y., Heath, L., Jensen, M.A., Rodrigo, A.G. and Mullins, J.I. Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes.  Evolutionary Bioinformatics Online 2:18-41.
Roy, S.W.  Intron rich ancestors.  Trends Genet 22, 468-71.
Roy, S. W., Ferreira, M. U. and Hartl, D. L. Evolution of allelic dimorphism in malarial surface antigens.  Heredity [epub online]: 1-8 doi: 10.1038/sj.hdy.6800887.
Roy, S.W. and Gilbert, W. The evolution of spliceosomal introns: patterns, puzzles, and progress.  Nat Rev Genet. 7(3): 211-221.
Roy, S.W., and Hartl, D.L. Very little intron loss/gain in Plasmodium: Intron loss/gain mutation rates and intron number.  Genome Research 16 (6): 750-756.
Roy, S.W., Manuel, I., and Penny, D. Very Little Intron Gain in Entamoeba histolytica Genes Laterally Transferred from Prokaryotes.  Mol. Biol. Evol. 23(10):1824–1827.
Roy, S.W., and Penny, D. Smoke Without Fire: Most Reported Cases of Intron Gain in Nematodes Instead Reflect Intron Losses.  Mol. Biol. Evol. 23(12):2259-2262.
Sainsbury, J.P., Greene, T.C., Moorhouse, R.J., Daugherty, C.H., and Chambers, G.K.   Microsatellite analysis reveals substantial levels of genetic variation but low levels of genetic divergence among isolated populations of Kaka (Nestor meridionalis). Emu 106: 329-338.
Santure, A.W., and Spencer, H.G. Influence of mom and dad: Quantitative genetic models for maternal effects and imprinting.  Genetics 173: 2297-2316.
Semple, C. and Steel, M. Unicyclic networks: compatibility and enumeration.IEEE/ACM  Transactions on Computational Biology and Bioinformatics 3(1), 84-91.
Shepherd, L.D. and Lambert, D.M. Nuclear microsatellite DNA markers for New Zealand kiwi (Apteryx spp.).  Molecular Ecology Notes 6: 227-229.
Sinclair, B.J., and Stevens, M.I. Terrestrial microarthropods of Victoria Land and Queen Maud Mountains, Antarctica: implications of climate change.  Soil Biology & Biochemistry, 38: 3158-3170 .
Slack, K.E., Jones, C.M., Ando, T., Harrison, G.L., Fordyce, E., Arnason, U. and Penny, D. Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution.  Molecular Biology and Evolution 23: 1144-1155.
Spencer, H.G. Evolution of genomic imprinting in mammals.  In Encyclopedia of Genomics, Proteomics and Bioinformatics, M. Dunn, L. Jorde, P. Little and S. Subramaniam (eds). John Wiley, Chichester, UK
Spencer, H.G., Brook, F.J. and Kennedy, M. Phylogeography of Kauri Snails and their Allies from Northland, New Zealand (Mollusca: Gastropoda: Rhytididae: Paryphantinae).  Molecular Phylogenetics and Evolution 38: 835-842.
Spencer, H.G., and Clark, A.G. A chip off the old block: A model for the evolution of genomic imprinting via selection for parental similarity.  Genetics 174: 931-935
Spencer, H.G., Dorn, T., and LoFaro, T. Population models of genomic imprinting. II. Maternal and fertility selection.  Genetics 173:2391-2398.
Steel, M. and Hein, J. Reconstructing pedigrees: a combinatorial perspective.  Journal of Theoretical Biology 240(3): 360-367.
Steel, M. and Pickett, K.M. On the impossibility of uniform priors on clade size. Molecular Phylogenetics and Evolution 39(2): 585-586. 
Steel, M. and Szekely, L. On the variational distance of two trees,  Annals of Applied Probability 16(3): 1563-1575.
Stevens, M.I., Fjellberg, A., Greenslade, P., Hogg, I.D., and Sunnucks, P. Redescription of the Antarctic springtail Desoria klovstadi using morphological and molecular evidence.  Polar Biology, 29: 820-830 .
Stevens, M.I., Greenslade, P., Hogg, I.D. and Sunnucks, P. Examining Southern Hemisphere springtails: could any have survived glaciation of Antarctica?  Molecular Biology and Evolution 23: 874-882.
Stevens, M.I., and Hogg, I.D. Contrasting levels of mitochondrial DNA variability between mites (Penthalodidae) and springtails (Hypogastruridae) from the Trans-Antarctic Mountains suggest long-term effects of glaciation and life history on substitution rates, and speciation processes. Soil Biology & Biochemistry, 38: 3171-3180 .
Stevens, M.I., Hogg, I.D. and Pilditch, C.A. Evidence for female-biased juvenile dispersal in corophiid amphipods from a New Zealand estuary.  Journal of Experimental Marine Biology and Ecology 331: 9-20.
Thatte, B.D. Invertibility of the TKF model of sequence evolution.  Mathematical Biosciences 200,(1): 58-75.
Towns, D.R., Atkinson, I.A.E., and Daugherty, C.H. Have the harmful effects of introduced rats on islands been exaggerated?  Biological Invasions 8(4): 863-891
Woodhams, M. Can Deleterious Mutations Explain the Time Dependency of Molecular Rate Estimates?  Mol. Biol. Evol., 23(12):2271-2273.
Zauner, S., Lockhart, P.J., Stoebe-Maier, B., Gilson, P., McFadden, G.I. and Maier, U.G. Differential Gene Transfers and Gene Duplications in Primary and Secondary Endosymbioses.  BioMed Central 6: 38.